We have previously reported that mild fluid percussion injury (FPI) is associated with a heightening of the hypothalamic-pituitary-adrenal axis response during the first post-injury weeks. This is the same time period when rehabilitative exercise has been strongly suggested to be ineffective. Here, we explored whether cardiac and temperature autonomic function may also be compromised during this early post-injury period. Following an FPI or sham injury, rats were exercised with forced (fRW) or voluntary (vRW) running wheels on post-injury days 0-4 and 7-11. Results indicated that overall activity levels were decreased and circadian rhythm was affected after FPI. Autonomic disruptions became evident when exercise was introduced, and these disruptions were dependent upon the characteristics of exercise. Elevations in heart rate (HR) and core body temperature (CBT) were observed as a response to vRW and fRW. FPI animals had more pronounced increases in HR as a result of vRW. Likewise, increases in HR were observed with fRW in all animals. A strong stress response has recently been associated with fRW exercise. FPI rats exposed to fRW were more responsive to experimental manipulations and had higher a CBT after the FRW session. The results suggest that subacute exercise, particularly if linked to a strong stress response, may be counterproductive. Here we show that cardiac and temperature autonomic function are compromised during the subacute period following a mild TBI.